Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI15899
Trapped Gene
Plekhc1 (ENSMUSG00000037712)
Vector Insertion
Chr 14: 46102242 - 46124171
Public Clones IST10545B9 (tigm)
Private Clones OST470668 (lexicon) OST462362 (lexicon) OST461404 (lexicon) OST460478 (lexicon)
OST459953 (lexicon) OST459938 (lexicon) OST459433 (lexicon) OST459295 (lexicon)
OST459114 (lexicon) OST458267 (lexicon) OST454309 (lexicon) OST453462 (lexicon)
OST453243 (lexicon) OST450630 (lexicon) OST445905 (lexicon) OST445663 (lexicon)
OST442998 (lexicon) OST349401 (lexicon) OST317483 (lexicon) OST232733 (lexicon)
OST70279 (lexicon) OST47529 (lexicon)
Severity of mutation (?) Insertion after 19% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000315015 (Chr14:46124172..46124405 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGATAAGTGTGGCATCCAG Chr14:46124308..46124327 59.52 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000315015 (Chr14:46124172..46124405 -)
Downstram Exon
ENSMUSE00000314890 (Chr14:46102107..46102241 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGATAAGTGTGGCATCCAG Chr14:46124308..46124327 59.52 50 CGCTTCGTCTTCAGACTGGT Chr14:46102122..46102141 60.59 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000453533 Chr14:46149611..46149713 No primer for this exon
upstream ENSMUSE00000706602 Chr14:46149609..46149793 No primer for this exon
upstream ENSMUSE00000408319 Chr14:46149100..46149266 GCTCTGGACGGGATAAGGAT Chr14:46149234..46149253 60.43 55
upstream ENSMUSE00000722177 Chr14:46149100..46149266 GCTCTGGACGGGATAAGGAT Chr14:46149234..46149253 60.43 55
upstream ENSMUSE00000315015 Chr14:46124172..46124405 TGGATAAGTGTGGCATCCAG Chr14:46124308..46124327 59.52 50

*** Putative Vector Insertion (Chr 14: 46102242 - 46124171) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000314890 Chr14:46102107..46102241 CGCTTCGTCTTCAGACTGGT Chr14:46102122..46102141 60.59 55
downstream ENSMUSE00000314881 Chr14:46095563..46095788 TATCCCAGGATTGCCTTCTG Chr14:46095633..46095652 60.03 50
downstream ENSMUSE00000315007 Chr14:46095248..46095350 TACTTGAATCGGAGCAGCAA Chr14:46095254..46095273 59.57 45
downstream ENSMUSE00000314872 Chr14:46092447..46092554 CTTCCGTGCATTCGATCTCT Chr14:46092454..46092473 60.36 50
downstream ENSMUSE00000314864 Chr14:46088915..46089049 GCAGCGTCAACTTCATCAAC Chr14:46088945..46088964 59.45 50
downstream ENSMUSE00000314991 Chr14:46088178..46088227 TCAGCAAGTTCTGGGATTGA Chr14:46088174..46088193 59.37 45
downstream ENSMUSE00000314985 Chr14:46087013..46087137 AGCAGGAGATGGACGTGTCT Chr14:46087045..46087064 59.87 55
downstream ENSMUSE00000314978 Chr14:46084759..46084865 ACAGCGAAGCCAGATCTCAT Chr14:46084743..46084762 59.98 50
downstream ENSMUSE00000314969 Chr14:46084399..46084620 TCAGATGCTGCATTTTCAGG Chr14:46084475..46084494 59.95 45
downstream ENSMUSE00000314959 Chr14:46081791..46081915 GCCAGGCTTGAATGAATCTC Chr14:46081809..46081828 59.78 50
downstream ENSMUSE00000314950 Chr14:46081442..46081583 GTCCATCCGAATCAACCTGT Chr14:46081498..46081517 59.79 50
downstream ENSMUSE00000706596 Chr14:46079428..46079698 ATTTTGGTCTTTCGCACGAG Chr14:46079554..46079573 60.25 45
downstream ENSMUSE00000336558 Chr14:46078467..46079698 ATTTTGGTCTTTCGCACGAG Chr14:46079554..46079573 60.25 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCGTATGCTTTCTGTTTCCT Chr14:46112190..46112211 59.9 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGCGTATGCTTTCTGTTTCCT Chr14:46112190..46112211 59.9 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CAGTGAATTTGCCCTTAAGCA Chr14:46112364..46112385 60.25 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CAGTGAATTTGCCCTTAAGCA Chr14:46112364..46112385 60.25 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037712